First introduced in the EX Team Rocket Returns expansion, Pokémon saw the return of Shining/Alternate Color Pokémon after their brief appearance in the Neo Revelation and Neo Destiny expansions. While they were still bound by the 1-per deck rule, they no longer featured multiple energy-type attacks (with the exception of Latias, Latios and Rayquaza from EX Deoxys) and often had very beneficial attacks, making them much more playable.

Their card design, like that of Pokémon-ex is also unique. The character art depicts the Pokémon with portions of their body protruding outside of the character window, almost as if they are "jumping out" of the card. Various areas of the card design have golden tinges added to it, such as the corners of the attack text box and character window; the shadows of these graphics are also holographic.

Like their predecessors, these cards were still difficult to obtain, the odds of finding one roughly 1 in 2 booster boxes, sending their prices soaring. By far the most valuable Pokémon are the Japanese versions of the Eeveelutions, which were awarded as tiered prize cards to members of the Pokémon Players Club. Complete sets and the higher tier cards still command high prices. Their subsequent English release in the EX Power Keepers expansion and POP Series 5 promotional set saw their initial demand decrease, though the Japanese World Champions Pack reprints of Vaporeon, Jolteon, and Flareon proved more popular than their original prints due to the distribution method of the set.

δ Delta Species Pokémon are always the type that their alternate-colored form takes on the color of. For example, Gyaradosδ is a Fire-type because Shiny Gyarados are red.

In the Diamond & Pearl expansion, Pokémon and Pokémon-ex were essentially jointly replaced by Pokémon LV.X, though Shiny Pokémon were again featured in the TCG in the Stormfront expansion. However, they received no special rules, multi-Energy attacks or visual enhancements. Their only difference from regular cards this time around was a special "starry" foil reminiscent of early English foil treatments (in Japan), or a unique collection number with the prefix "SH" (outside Japan). This change perhaps reflects that in the Pokémon games, Shiny Pokémon are no different to normal Pokémon, other than that they are a different color.

Pokémon that have appeared as Pokémon

Pokémon Cards listed with a blue background are only legal to use in the current Expanded format.Cards listed with a silver background are legal to use in both the current Standard and Expanded formats.